However, I am having a problem where when I set my structured application this way, the import command still prompts me for the structured application. Obviously, I want to avoid the prompt since I am supplying the application name.

I think you also need to tell FM that the document to be imported is an XML document. Set Constants.FS_ImportAsType to Constants.FV_TYPE_XML as well as defining the structured application. That should do the trick. Let me know if it works.